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- PDB-4lbs: Crystal structure of human AR complexed with NADP+ and {2-[(4-bro... -

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Basic information

Entry
Database: PDB / ID: 4lbs
TitleCrystal structure of human AR complexed with NADP+ and {2-[(4-bromo-2,6-difluorobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-4O8 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.76 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Fanfrlik, J. / Kolar, M. / Hobza, P. / Podjarny, A.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Modulation of aldose reductase inhibition by halogen bond tuning.
Authors: Fanfrlik, J. / Kolar, M. / Kamlar, M. / Hurny, D. / Ruiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Rezac, J. / Munusamy, E. / Lepsik, M. / Matejicek, P. / Vesely, J. / Podjarny, A. / Hobza, P.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0763
Polymers35,8981
Non-polymers1,1782
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.297, 66.903, 47.304
Angle α, β, γ (deg.)90.000, 92.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-4O8 / {2-[(4-bromo-2,6-difluorobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid


Mass: 434.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11BrClF2NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO UNIPROT SEQUENCE DATABASE, THERE IS A L->I SEQUENCE CONFLICT AT THIS POSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM ammonium citrate, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.70849 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 0.76→50 Å / Num. all: 349645 / Num. obs: 349645 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.043 / Χ2: 1.047 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
0.76-0.792.90.301273131.022172.9
0.79-0.823.40.261309621.016182.9
0.82-0.8640.208343551.046191.6
0.86-0.94.50.157354401.087194.6
0.9-0.964.90.113362691.077196.8
0.96-1.035.70.085360721.101196.2
1.03-1.146.70.064368481.041198.2
1.14-1.36.60.05371841.009198.9
1.3-1.646.60.043374611.035199.6
1.64-506.40.034377411.031199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1US0

1us0


Resolution: 0.76→38.601 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9459 / SU ML: 0.04 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 11.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1337 17605 5.04 %Random 5%
Rwork0.132 ---
obs0.132 349624 93.08 %-
all-349624 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.95 Å2 / Biso mean: 12.1739 Å2 / Biso min: 2.38 Å2
Refinement stepCycle: LAST / Resolution: 0.76→38.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 73 592 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072714
X-RAY DIFFRACTIONf_angle_d1.3923710
X-RAY DIFFRACTIONf_chiral_restr0.085409
X-RAY DIFFRACTIONf_plane_restr0.008471
X-RAY DIFFRACTIONf_dihedral_angle_d12.3721034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.76-0.76820.22513780.22017880825866
0.7682-0.77720.18964410.20368708914973
0.7772-0.78670.21154750.19199189966477
0.7867-0.79670.17825130.181994971001080
0.7967-0.80720.17184900.176796651015581
0.8072-0.81820.15195430.1585102791082287
0.8182-0.82990.1516030.1486105731117689
0.8299-0.84230.14615750.1401108981147392
0.8423-0.85550.13475620.1353111611172394
0.8555-0.86950.14465850.1303111651175094
0.8695-0.88450.13146120.1266110601167293
0.8845-0.90060.12726250.1219114061203196
0.9006-0.91790.12436510.1139114741212597
0.9179-0.93660.11625960.1093114361203297
0.9366-0.9570.11056120.1079115641217697
0.957-0.97930.11746090.1078113261193596
0.9793-1.00370.11096020.1037113161191895
1.0037-1.03090.09826450.1019115741221998
1.0309-1.06120.10586200.1116611228198
1.0612-1.09550.10096000.099117241232498
1.0955-1.13460.09926620.1012116021226498
1.1346-1.18010.09736190.1012117681238799
1.1801-1.23380.10446220.1069117561237899
1.2338-1.29880.12045930.1141118661245999
1.2988-1.38020.12066310.119118061243799
1.3802-1.48680.12046250.1251190912534100
1.4868-1.63640.12926080.12651191212520100
1.6364-1.87320.14516380.14181189912537100
1.8732-2.360.16366100.15551201212622100
2.36-38.65070.15666600.1585119331259399

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